The reason for the deprecation was because whilst the majority of websites used SHA1 it was weak and prone to attack. Since 2014 the likes of Google and Microsoft announced that they would begin to deprecate SHA1 on their web browsers which may cause browser compatibility issues with websites still using SHA1.
If users report they get the above message when trying to launch a published application or desktop via NetScaler Gateway it may be because the certificate you have installed on the NetScaler Gateway is of the SHA2 family and the user is still using an old version of Citrix Receiver. SSL Error 61: You have not chosen to trust “Certificate”, the issuer of the server’s security certificate.
Contact your help desk with the following information: Cannot connect to the Citrix XenApp server.